June 27, 2017
My name is rob and I love fish and kelp
Devise a fancy question and call it a hypothesis
Formulate a means of collecting the relevant data
Import data set into statistical software package
Run the procedure to get results
Copy and paste appropriate pieces from the analysis into document editor
Add descriptions
Finish/submit report for comments
REPEAT steps 2 - 7 after receiving comments indefinately..
The process of data capture is not open
Lots of manual work (prone to make errors)
Tedious (who likes to carefully copy-and-paste?)
Likely not recordable (did you write down all the steps you followed to get your analysis?)
What if you made an error at the beginning of your analysis? If your data had an error? If your hypothesis was biased?
R is a free software package for statistical analysis and graphics.
R is an older version that favours the command line programmer
RStudio is a powerful user interface that helps you get better control of your analysis.
Like R, it is also completely free.
You can write your entire paper/report (text, code, analysis, graphics, etc.) all in a language called R Markdown.
If you need to update any of your code, R Markdown will automatically update your plots and output of your analysis and will create an updated PDF file.
No more copy-and-paste!
“Literate programming”
Embed R code in a Markdown document
Renders textual output along with graphics
Bookdown is one of the more recent additions to the R-universe.
Some highlights are:
Multiple output formats
Focus on writing the content not typesetting
Readers can interact with examples
Feedback and contributions as the book is developed
Integrates with version control
Thesisdown is built from bookdown
The current output for the four versions is here:
You can now increase your online voice using tools developed in your research methods and present them as a blog!
blogdown allows you to create websites using R MarkdownThe website is generated from R Markdown documents
can be computed and rendered dynamically from R code to your website!
Git is a version control system that lets you track changes to files over time
Github is a website for storing your git versioned files remotely
Github provides a home for your Git-based projects on the internet
If you are a student you can get the micro account which includes 5 private repositories for free!
“Let us change our traditional attitude to the construction of programs: Instead of imagining that our main task is to instruct a computer what to do, let us concentrate rather on explaining to humans what we want the computer to do.”
Donald Knuth, Literate Programming (1984)
“Reproducible research is the idea that data analyses, and more generally, scientific claims, are published with their data and software code so that others may verify the findings and build upon them.”
Roger Peng, Johns Hopkins